Detailed knowledge on the distribution and abundance of a particular population or species over time is an important prerequisite for the implementation of effective conservation strategies. Monitoring of rare and elusive species, such as large European carnivores, however, is particularly difficult. In this project we develop and apply molecular marker systems for non-invasive genetic monitoring of rare European wildlife species. The analyses, mostly based on hair or scat samples, allow for detailed insights regarding species identity, hybridization status, sex, and population assignment. Molecular tools are currently developed for the following species: Wildcat (Felis silvestris), Eurasian lynx (Lynx lynx), wolf (Canis l. lupus), brown bear (Ursus arctos), and European beaver (Castor fiber). Investigation of spatial genetic patterns within the species’ ranges will allow to assess dispersal propensities and migration corridors. In combination with the application of habitat modelling approaches, these data will allow to predict the impact of Climate Change on distribution and viability of these European flag ship species and form a solid scientific base for the implementation of effective conservation strategies.